Course-based Research Experience Research Articles

Introductory course-based research experience for university sophomores: Using testicular-feminized mice to identify genes underlying brain sexual differentiation

Like many educators, we are striving to incorporate more active learning and inquiry-driven exercises into our STEM curricula. Course-based undergraduate research experiences (CUREs) have become more common in undergraduate laboratory courses in many STEM fields. Here we detail a new CURE developed in a sophomore-level undergraduate molecular neuroendocrinology course at California State University Long Beach. The course centered on the mouse model carrying testicular feminization mutation ( Tfm). This mutation, resulting from a single base deletion, produces a nonfunctional androgen receptor (AR) protein. Thus, Tfm mice are insensitive to androgen through ARs, providing an excellent model to probe the physiological role of ARs in the development of the brain and behavior. Since AR is the main mediator of androgen activity by acting as a hormonal transcription regulator, gene expression profiling has been measured in the brains of Tfm mice and normal controls to identify the potential AR-regulated genes as downstream molecular effectors. Our CURE took a similar approach, aiming to determine (1) if the selected genes were expressed differentially between the sexes and (2) if their expression could be altered by loss of AR in specific brain regions. Three broad goals of having students think, communicate, and perform like scientists were organized in the learning objectives for the CURE. All participating students (n=21) were pursuing a biology or related major, and none had any experience conducting independent laboratory research. Here students first used polymerase chain reaction (PCR) genotyping to screen the mice carrying the Tfm mutation and their sexes. They next conducted a literature search and review, through which they learned how to select databases and how to combine key words to create a productive search string for identifying the potential AR-regulated genes. Last, students performed RT-qPCR in the wild-type and Tfm mouse hypothalamus and measured sex- and AR-dependent gene expression. These modules cover not only key concepts in genetics, molecular biology, and neuroendocrinology, but also the development of methods and techniques, including DNA/RNA extraction, electrophoresis, and RT-PCR/qPCR. We designed the CURE for a semester timeline with a single three-hour laboratory section meeting once a week for 15 weeks. All modules were taught and conducted in a research laboratory containing all materials and equipment necessary for research. At the end, students constructed and presented posters on their results. To assess how well students achieved the learning goals, we administered pre- and post-course surveys. Students reported striking gains related to the learning goals, with a high degree of satisfaction. Students also perceived the improved understanding of the scientific backgrounds and methods in the CURE. This CURE course illustrates that authentic research experiences, which use complex molecular techniques, can be offered to sophomore students. The course can serve as a template to ignite students’ intellectual curiosity and improve their understanding of the scientific process by engaging them in novel research. This work was supported by the Keck Undergraduate Research Experiences (KURE) Incubator funding. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Exponential Fit to Food Degradation Experiment

Students in the Principles of Biology I course use a lot of course time preparing solutions each week in their coursebased research experience. This experiment was designed to determine the degradation rates of prepared solutions ofvarious plant-based foods (i.e., Napa cabbage, rice, peanuts, and apple) under refrigeration as a means of reducing theamount of time for solution preparation. Scaling from the original lab procedures, approximately sixty milliliters offiltrate were prepared from the listed foods and testing was conducted on a thrice-weekly schedule. The concentrationof proteins and carbohydrates were measured using the Bradford’s assay and Benedict’s test, respectively. The datarevealed a noticeable trend in degradation in protein for all the samples. The rice sample proved to be an outlier witha marked increase in reducing sugars, while the other samples gradually decreased.

Are Showerhead Filters Retailed Online a Scam? Investigating Water Quality Claims Through a Course-Based Research Experience

Are Showerhead Filters Retailed Online a Scam? Investigating Water Quality Claims Through a Course-Based Research Experience

Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework.

We have developed a flexible undergraduate curriculum that leverages the place-based research of environmental microbiomes to increase the number of Indigenous researchers in microbiology, data science and scientific computing. Monitoring Environmental Microbiomes (MEM) provides a curriculum and research framework designed to integrate an Indigenous approach when conducting authentic scientific research and to build interest and confidence at the undergraduate level. MEM has been successfully implemented as a short summer workshop to introduce computing practices in microbiome analysis. Based on self-assessed student knowledge of topics and skills, increased scientific confidence and interest in genomics careers were observed. We propose MEM be incorporated in a scalable course-based research experience for undergraduate institutions, including tribal colleges and universities, community colleges and other minority serving institutions. This coupled curricular and research framework explicitly considers cultural perspectives, access and equity to train a diverse future workforce that is more informed to engage in microbiome research and to translate microbiome science to benefit community and environmental health.

Development and Implementation of a Bioinnovation Focused Course-Based Research Experience for Undergraduate Students

Development and Implementation of a Bioinnovation Focused Course-Based Research Experience for Undergraduate Students

Experimental Mathematics – A Course-Based Research Experience in Machine Learning

Efforts to expand the science, technology, engineering and mathematics (STEM) work- force have been topics of United States policy action for more than 50 years (Hira 2010). Unfortunately, among U.S. undergraduate curricula, STEM has one of the highest attrition rates (Tinto 1993) with less than half of students in the U.S. that enroll in an undergraduate STEM program ultimately receiving a degree in a STEM field (Hayes 2009). Naturally, the high rate of attrition is a topic of persisting concern. Many programs have been designed and implemented to model best practices in retaining students in STEM disciplines. One retention strategy is to engage STEM undergraduates in research experiences, and a number of programs have been implemented to provide such experiences. The Towson University Research Enhancement Program (TU REP) is one such program. This cohort-based program supports faculty in the development of course-based undergraduate research experiences (CUREs). In this note we describe a CURE in machine learning offered by the Towson University Department of Mathematics whose development was supported by TU REP. We categorize this course along the spectrum of traditional, inquiry, CURE and internship in each of the five dimensions characteristic of a CURE.

Problem Solving for Teachers – Action Research in a Cross-Listed Undergraduate and Graduate Course

This article describes a course-based research experience in a cross-listed mathematical problem solving course for middle school pre-service and in-service teachers. The course was conducted entirely online due to statewide and university restrictions during the coronavirus pandemic. This study examines 4 undergraduate and 5 graduate students’ understanding of mathematical modeling. Undergraduate and graduate students were paired in groups to develop open-ended model-eliciting activities for their classmates to solve, and groups conducted educational action research to analyze their classmates’ work on the activities. We present one group’s activities and their results as an example of how action research can be conducted in a virtual teaching environment.

Course-Based Research Experience to Introduce Engineering Students to Research Aimed at Innovation in Early Years

Course-based undergraduate research experiences (CUREs) increase research exposure and may exert a strong influence on students’ academic and career paths. However, very few CUREs are documented within the entry years of the engineering curricula. In this work, we describe the design, implementation, and evaluation of a CURE-based introductory-level engineering elective, to introduce second-year chemical and petroleum engineering students not only to research but more importantly to the fields of innovation and entrepreneurship. In contrast to more traditional CUREs, this course focuses on the innovation pathway, using concepts from engineering design and from scientific research as tools to solve real-world scientific problems. This innovation-focused CURE has proven to be an effective way to expand research experiences, in particular for engineering students who typically have limited opportunities to participate in hypothesis-driven research aimed at innovation during the introductory years of their undergraduate education.

Proteins with Known Structure but Previously Unknown Function Identified as Hydrolases

The Protein Data Bank (PDB) contains the structures of over 4000 proteins of unknown function. In an attempt to assign function to some of these structures we combined in silico and in vitro analyses focusing on those most likely to be of the hydrolase class. We used bioinformatics tools including active site‐alignment software, BLAST, Pfam, and Dali to predict putative protein functions. We expressed and purified the proteins and carried out in vitro activity assays, informed by the in silico‐predicted enzyme function. We present data confirming the in vitro hydrolase function of several proteins of known structure but previously unidentified function. These studies used the Biochemistry Authentic Scientific Inquiry Lab (BASIL) modules as a framework and were carried out as part of an undergraduate course‐based research experience (CURE).

A CURE for Cloning: Implementing a Modular Approach to Cloning Recombinant Antibodies in an Undergraduate Teaching Lab

An undergraduate course‐based research experience (CURE) is a high impact practice which provides genuine research experiences to a large and diverse student population. We have implemented a six‐week research module involving the cloning and expression of therapeutic antibodies as the culmination of a senior level Biochemistry lab course. We have designed a cloning system that takes advantage of the modular domain structure of antibodies to facilitate changes to an antibody’s affinity, isotype, or allotype. Specifically, our system was developed for readily swapping the antigen‐binding N‐terminal sequences of different antibodies into a set of vectors encoding the conserved regions of the heavy and light chains, all in the background of a strong mammalian expression vector. Gene fragments corresponding to the constant regions of each immunoglobulin chain, as well as the antigen‐binding regions of unique antibodies were designed, and produced by gene synthesis. Various iterations of the module were tested over four different semesters with high levels of success in terms of student engagement and research goals. The resulting plasmid constructs are now being used by our research lab as part of the investigation of the nature of antibody recognition of cancer‐specific Mucin antigens. This project allowed our senior undergraduates to contribute to an active research program, while earning credit toward a required course. It exposed them to modern cloning methodologies, bioinformatics tools, cell culture techniques and participation in a local research conference. It is also a readily scalable project as only the variable regions of new antibodies of interest need be synthesized.

Creating a Learning Model Where Students Practice the Scientific Process Through Protein Modeling

Based on the CREST (Connecting Researchers, Educators, and STudents) model undergraduate students at Nova Southeastern University (NSU) cooperated in teams through a specially designed Honors Seminar Course titled, “Introduction to Protein Modeling”. This Course‐based Undergraduate Research Experience (CURE) brought together groups of undergraduate students early in their studies to have authentic research and presentation experiences. This course was open to all students in NSU’s Farquhar Honors College regardless of their major, academic level or previous college level experience with science or protein modeling. Out of 15 registered students, seven of them were first semester freshmen, one was a sophomore, three were juniors, and four were seniors. Most of the students were Biology or Behavioral Neuroscience Majors. However, there was one of each of the following four majors: Dance, Exercise and Sport Science, Marine Biology, and Pre‐Nursing. The students were divided into five groups of three, each consisting of a mix of freshmen and upper‐level students. Here we present the design and results of a course that provided students with early access to a course‐based research experience using various protein bioinformatics tools (Jmol, Pymol, Autodoc Vina, and the Protein Data Bank). Students were shown previously completed projects as part of the CREST Program available on the Program’s website: https://cbm.msoe.edu/crest/new9_2021.php. To support CURE sustainability, we used an interdisciplinary team‐teaching approach, with distributed leadership and the support of the University’s Honors College in the development of this course. Students worked collaboratively during class meetings to identify a protein molecular story that they wanted to research and describe using molecular modeling tools, including the development of a 3‐D model. At the midterm, the student groups shared their progress and received feedback from the faculty and their peers. Students continued to revise their modeling projects and received additional feedback one month later. At the end of the semester each team presented their final projects with components that included a protein model description sheet, poster, and oral presentations. Student projects included molecular stories related to MMP 12, cystic fibrosis transmembrane regulator, marine bacterial laminarinase, sickle cell anemia, and iron acquisition in E. coli related to TonB/TonBox binding. Through interacting with the primary literature, course materials, and using protein modeling tools, students gained an introduction to the scientific process and applied it to better understand molecular mechanisms. During this process, students also learned to explain these processes to themselves and others through constructing presentations and model descriptions. Student learning gains were documented by using the RISC (Research on the Integrated Science Curriculum) Survey.

Instructional Models for Course-Based Research Experience (CRE) Teaching.

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.

Real-time text message surveys reveal student perceptions of personnel resources throughout a course-based research experience.

Course-based research experiences (CREs) are designed to engage students in authentic scientific experiences that are embedded into a standard curriculum. CREs provide valuable research experiences to large numbers of undergraduate biology students, however, CRE implementation can require many personnel. Because limited personnel may be a barrier to widespread CRE implementation, our goal was to discover which personnel students valued throughout a CRE and the ways they were valuable. We investigated students’ perceptions of personnel resources throughout a semester-long CRE using two survey approaches. Using a text message survey administered multiple times per week, real-time data was collected about which personnel resource students perceived to be the most helpful. Using a web-based survey administered five times throughout the semester, retrospective data was collected about how often students used each personnel resource and how helpful students perceived each personnel resource to be. Graduate teaching assistants (TAs) were consistently selected as the most helpful personnel resource by the majority of respondents throughout the semester, with most respondents describing graduate TAs providing project-specific feedback. Although less frequently, undergraduate TAs were also consistently selected as the most helpful personnel resource. Respondents described undergraduate TAs providing project-specific feedback, general feedback, and project-specific resources. Data from the retrospective, web-based survey largely mirrored the real-time, text message survey data. Throughout the semester, most respondents reported using graduate TAs “Often” or “Always” and that graduate TAs were “Very” or “Extremely” helpful. Throughout most of the semester, most respondents also reported using undergraduate TAs “Often” or “Always” and that undergraduate TAs were “Very” or “Extremely” helpful. The results of this descriptive study underscore the importance of graduate and undergraduate TAs in the development and implementation of CREs, emphasizing the need for departments and course coordinators to be intentional in planning TA training that prepares TAs to fulfill their critical role in CRE implementation.

Complete Genome Sequences of Four Putatively Antibiotic-Producing Bacteria Isolated from Soil in Arkansas, USA.

ABSTRACTSoil bacteria can be a valuable source of antimicrobial compounds. Here, we report the complete genomes of four soil bacteria that were isolated by undergraduate microbiology students as part of a course-based research experience. These genomes were assembled using a hybrid approach combining paired-end Illumina reads with Oxford Nanopore Technologies MinION reads.

Broadening Participation through Research Experiences in Marine Science: An Early-Admit Immersive College Course Provides Experiential, Place-Based Scientific Training for Hawai‘i High School Students

Developing meaningful and authentic opportunities for students from historically excluded groups that inspire and sustain their interest in STEM pathways is essential for overcoming some of the barriers to entry that continue to hinder diversity in STEM fields. The Research Experiences in Marine Science (REMS) program is an immersive, place-based, course-based research experience at the University of Hawai‘i at Mānoa that focuses on science-driven marine conservation and incorporates Hawaiʻi’s unique ecology and culture to better engage local high school students and recent high school graduates. During the program, students participate in field- and laboratory-based marine science modules and conduct research alongside professional scientists, science educators, and near-peer mentors, and they are encouraged to consult with Native Hawaiian scholars and practitioners who actively collaborate or partner with the program. Student self-assessments of confidence, attitudes, and interest in marine science were collected pre- and post-program via surveys that included both Likert scale and open-ended items. Results demonstrated significant positive post-program shifts in student confidence in testing hypotheses, valuing environmental stewardship, and recognizing the relevance of marine science, as well as shifts in the students’ interest in marine science subjects and careers. Students reported very high satisfaction with the content modules, group research projects, and overall REMS program experience. Our approach, emphasizing sense of place, community connections, and a strong tiered mentoring structure, provides a robust model for undergraduate science training that may help broaden student participation in conservation-related marine STEM.

Abstracts

Abstracts

Effect of Music on a Mindfulness Experience: An Online Study

Mindfulness has become increasingly common in therapeutic and non-therapeutic venues as a way to address stress, change, and uncertainty, such as in the COVID-19 pandemic. The use of music in mindfulness is apparent in several traditional and Western practices but has little research regarding its effect in novice practitioners. In an online course-based research experience, a group of student researchers, a graduate research assistant and two faculty members recruited 54 healthy participants within their social networks, to investigate the effect of a music stimulus on one mindfulness exercise and the feasibility of implementing this intervention in virtual sessions. Participants attended two virtual group sessions where student researchers and a faculty member/research assistant provided online questionnaires and links to a 20-minute meditation recording, either with or without music, as the two conditions. Potential moderators of the intervention included stress in the previous month and absorption in music. A repeated-measures ANCOVA indicated no significant differences among conditions, and no interaction with stress or absorption in music. Although contrary to our expectations, the lack of significant differences between conditions indicate that music did not distract from a mindfulness meditation, and that the music and guided mindfulness stimulus was as efficacious as the guided mindfulness alone. Given the potential for music to become a distractor for novice practitioners, this finding is important and in line with our theoretical framework. Online delivery of this intervention was feasible and apparently effective. Suggestions for implementation of online research and intervention delivery are included.

A functional genomics screen identifying blood cell development genes in Drosophila by undergraduates participating in a course-based research experience.

Undergraduate students participating in the UCLA Undergraduate Research Consortium for Functional Genomics (URCFG) have conducted a two-phased screen using RNA interference (RNAi) in combination with fluorescent reporter proteins to identify genes important for hematopoiesis in Drosophila. This screen disrupted the function of approximately 3500 genes and identified 137 candidate genes for which loss of function leads to observable changes in the hematopoietic development. Targeting RNAi to maturing, progenitor, and regulatory cell types identified key subsets that either limit or promote blood cell maturation. Bioinformatic analysis reveals gene enrichment in several previously uncharacterized areas, including RNA processing and export and vesicular trafficking. Lastly, the participation of students in this course-based undergraduate research experience (CURE) correlated with increased learning gains across several areas, as well as increased STEM retention, indicating that authentic, student-driven research in the form of a CURE represents an impactful and enriching pedagogical approach.

Creating Children’s Books to Promote Exposure and Build Communication Skills in Engineering

In an attempt to overcome barriers faced by engineering students, a strengths-based approach to an Introduction to Engineering course was developed and deployed at a minority-serving institution in the US Midwest. This course-based research experience provided an environment that allowed students to learn about various engineering disciplines and improve their communication skills while engaging in a constructivist-grounded process. Students were asked to construct their knowledge and make meaning of the engineering disciplines through the creation of a children’s book that introduced young readers to engineering. Although book creation in an engineering course may seem unconventional to many, this course produced students with sound communication skills and a fundamental understanding of engineering that has laid the foundation for their academic careers.

Research in the Classroom: Introducing Nanomaterials at a Two-Year College

This article illustrates how the authors transformed “research in the classroom” into chemistry courses at a two-year college in the form of short course-based research experience. The students worked in groups to research nanomaterials, came up with a series of carbon nanoparticles precursors from waste materials, and developed simple and cost-effective methods to produce carbon nanoparticles. Not surprisingly, students became more active learners as they were in charge of learning, and were given authority to modify lab activities with their learning experience progressing. A deeper approach to learning helped students better appreciate chemical sciences, increase conceptual learning, and become responsible citizens. The project also provided a platform to discuss sustainability, green chemistry, and nanomaterials. To increase the efforts for student success, academic technologies were utilized to aid the project.